hasTautomers

handlesMultiFragmentMolecules

public boolean handlesMultiFragmentMolecules()

Returns true if the plugin handles multifragment molecules,
false otherwise. In the latter case the plugin takes the
fragment with more atoms if a multifragment molecule is given as input.
Returns true if parameter "single" is set to "false",
false otherwise (default: false).

setCleanResultStructures

@Deprecated
public void setCleanResultStructures(boolean clean)

Deprecated.obsolate method

Sets 2D cleaning of the result structures: if true then the changed atoms in
tautomers returned by getStructure(int) are partial cleaned in 2D.
Should be called before setting input molecule.
Default: false.

Parameters:

clean - if true then result structures are cleaned in 2D

Since:

Marvin 5.1.2

getChangedAtomIndexes

public int[] getChangedAtomIndexes()

Returns the indexes of the atoms changed during tautomerization. Should be called after
run(). Returns null if none of the atoms has changed.
For internal use only.

Returns:

the indexes of the changed atoms

Since:

Marvin 5.12

setSymmetryFiltering

public void setSymmetryFiltering(boolean filtering)

Sets symmetry fitlering: if true then symmetrical structures
are filtered out, otherwise symmetrical structures are returned as duplicates.
Symmetry filtering is always performed when canonical tautomer form is taken,
regardless of the actual setting of the filtering parameter.
Default: true.

setMaxStructureCount

public void setMaxStructureCount(int max)

Sets the maximum number of structures to be generated. This number is the
sum of unique tautomeric count and degenerated tautomeric count.
Note: getStructure(int) returns only the unique tautomers,
getStructureCount() returns unique tautormer count.
Default: 1000.

Parameters:

max - is the maximum number of structures to be generated

Since:

Marvin 4.1

setpH

public void setpH(double pH)

Sets the pH to be considered in dominant tautomer generation. By default,
no pH effect considered (Double.NaN).

setProtectLabeledTetrahedralStereoCenters

Sets the protection of labeled tetrahedral stereo centers: if true then labeled tetrahedral stereo
centers are protected by the tautomer generator. Has no effect in case of generic tautomer.
Default: false.

Parameters:

protect - is true if labeled tetrahedral stereo centers should be protected by the tautomer
generator

Since:

Marvin 5.1

setProtectEsterGroups

public void setProtectEsterGroups(boolean protect)

Sets the protection of ester groups: if true then ester groups are excluded from the tautomerization.
Default: true. Has no effect in case of generic tautomer.

Parameters:

protect - is true if ester groups should be excluded from the tautomerization

getDominantTautomerDistribution

public double getDominantTautomerDistribution(int index)

Returns the distribution of the dominant tautomer. Dominant tautomers are
ordered by distribution: first (index = 0) is the major
tautomer with largest distribution, followed by other dominant tautomers
in descending distribution order. Use getStructure(int) to get the
dominant tautomer structure.

getNewOldIndexMap

public int[] getNewOldIndexMap()

Returns:

the index mapping relations between the implicit-explicit molecule forms
new -> old mapping , atom indexing starts form "0"
e.g. if the "2" is the new index in the implicitized form then
the "map[2]" will be the old index in the explicit form

getOldNewIndexMap

public int[] getOldNewIndexMap()

Returns:

the index mapping relations between the explicit- implicit molecule forms
old -> new mapping , atom indexing starts form "0"
e.g. if the "2" is the old index in the explicit form then
the "map[2]" will be the new index in the implicitized form